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Configuration Parameters

These are additional configuration parameters that are not primary pipeline inputs.

database_sets

Type: array

Default: ["ncbi_16s_18s:[reference:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/ncbi_16s_18s/ncbi_targeted_loci_16s_18s.fna'", "database:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/ncbi_16s_18s/ncbi_targeted_loci_kraken2.tar.gz'", "ref2taxid:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/ncbi_16s_18s/ref2taxid.targloci.tsv'", "taxonomy:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/ncbi_16s_18s/new_taxdump_2025-01-01.zip']", "ncbi_16s_18s_28s_ITS:[reference:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna'", "database:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS_kraken2.tar.gz'", "ref2taxid:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/ncbi_16s_18s_28s_ITS/ref2taxid.ncbi_16s_18s_28s_ITS.tsv'", "taxonomy:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/ncbi_16s_18s_28s_ITS/new_taxdump_2025-01-01.zip']", "SILVA_138_1:[reference:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/SILVA_138_1/silva.fna'", "database:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/SILVA_138_1/kraken2.tar.gz'", "ref2taxid:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/SILVA_138_1/seqid2taxid.map'", "taxonomy:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/SILVA_138_1/taxonomy.tar.gz']", "Greengenes2_plus:[reference:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/Greengenes2_plus/sequences_mm2format.fasta'", "database:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/Greengenes2_plus/kraken2.tar.gz'", "ref2taxid:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/Greengenes2_plus/sequences_mm2format.taxid.map'", "taxonomy:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/Greengenes2_plus/taxdump.tar.gz']", "Standard-8':[database:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/Standard-8/k2_standard_08gb_20241228.tar.gz", "taxonomy:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/taxonomy/new_taxdump_2025-01-01.zip']", "PlusPF-8':[database:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/PlusPF-8/k2_pluspf_08gb_20241228.tar.gz", "taxonomy:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/taxonomy/new_taxdump_2025-01-01.zip']", "PlusPFP-8':[database:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/PlusPFP-8/k2_pluspfp_08gb_20241228.tar.gz", "taxonomy:'s3://ont-open-data/workflow-databases/wf-metagenomics-dbs/taxonomy/new_taxdump_2025-01-01.zip']"]

schema_ignore_params

Type: string

Default: show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,database_sets,wf

wf.example_cmd

Type: array

Default: ["--fastq \\'wf-metagenomics-demo/test_data\\'"]

wf.agent

Type: string

wf.container_sha

Type: string

Default: sha38db033c15c74ae7cac3c609fdfe2c8d2a53ef6f

wf.common_sha

Type: string

Default: shafdd79f8e4a6faad77513c36f623693977b92b08e

wf.container_sha_amr

Type: string

Default: shad8ebf2fc3b15d43612df71170bdd4d8669fe1731

This pipeline was built with Nextflow. Documentation generated by nf-docs v0.1.0 on 2026-01-23 17:27:31 UTC.